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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ), 'gf_id' => 'HOM05D001084', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001084' ), 'data_identifier' => 'HOM05D001084', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001084', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '566', 'num_species' => '95' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p28990' => 'bna', 'A03p32900' => 'bna', 'A03p62830' => 'bna', 'A04p04010' => 'bna', 'A07p02020' => 'bna', 'A07p17290' => 'bna', 'A07p35280' => 'bna', 'A07p35290' => 'bna', 'A07p35300' => 'bna', 'A08p16940' => 'bna', 'A09p09860' => 'bna', 'A09p12010' => 'bna', 'Aa31LG1G15200' => 'aar', 'Aa31LG1G15210' => 'aar', 'Aa31LG2G16200' => 'aar', 'Aa31LG8G15440' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_228.1854' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.223' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_344.224' => 'aag', 'Actinidia00498' => 'ach', 'Actinidia00499' => 'ach', 'Actinidia08238' => 'ach', 'Actinidia15949' => 'ach', 'Actinidia15950' => 'ach', 'Actinidia17827' => 'ach', 'Actinidia19159' => 'ach', 'Actinidia22487' => 'ach', 'Actinidia27911' => 'ach', 'Ah.02g126440' => 'amhyb', 'Ah.03g139640' => 'amhyb', 'AL3G51980' => 'aly', 'AL5G17760' => 'aly', 'AL5G17790' => 'aly', 'AL5G17800' => 'aly', 'AL5G22150' => 'aly', 'AL5G38590' => 'aly', 'AL7G16940' => 'aly', 'AL7G16950' => 'aly', 'AL7G46690' => 'aly', 'AL8G44810' => 'aly', 'AL8G44820' => 'aly', 'AL8G44830' => 'aly', 'Aqoxy5G00908' => 'aox', 'Aqoxy5G01705' => 'aox', 'Aqoxy6G01019' => 'aox', 'arahy.Tifrunner.gnm1.ann1.850ERF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.NQI65D' => 'arhy', 'AT2G18630' => 'ath', 'AT3G28270' => 'ath', 'AT3G28290' => 'ath', 'AT3G28300' => 'ath', 'AT3G28310' => 'ath', 'AT3G28320' => 'ath', 'AT3G57100' => 'ath', 'AT4G34320' => 'ath', 'AT4G34330' => 'ath', 'AT5G66660' => 'ath', 'AT5G66670' => 'ath', 'AT5G66675' => 'ath', 'ATR0733G149' => 'atr', 'Atru.chr3.511' => 'acertr', 'Atru.chr5.2940' => 'acertr', 'Atru.chr5.2941' => 'acertr', 'AUR62003196' => 'cqu', 'AUR62003197' => 'cqu', 'AUR62008013' => 'cqu', 'AUR62008014' => 'cqu', 'AUR62011358' => 'cqu', 'AUR62016703' => 'cqu', 'BcaB02g10002' => 'bca', 'BcaB02g10003' => 'bca', 'BcaB02g10004' => 'bca', 'BcaB03g11840' => 'bca', 'BcaB03g15860' => 'bca', 'BcaB03g15861' => 'bca', 'BcaB03g15862' => 'bca', 'BcaB03g16654' => 'bca', 'BcaB04g20112' => 'bca', 'BcaB06g26055' => 'bca', 'BcaB07g30176' => 'bca', 'BcaB07g31653' => 'bca', 'BcaC01g00914' => 'bca', 'BcaC01g04450' => 'bca', 'BcaC01g04547' => 'bca', 'BcaC02g09806' => 'bca', 'BcaC02g09808' => 'bca', 'BcaC02g09821' => 'bca', 'BcaC02g09825' => 'bca', 'BcaC04g22894' => 'bca', 'BcaC04g23147' => 'bca', 'BcaC06g34729' => 'bca', 'BcaC06g34730' => 'bca', 'BcaC06g36440' => 'bca', 'BcaC08g46341' => 'bca', 'BcaC08g46342' => 'bca', 'BcaNung06126' => 'bca', 'BolC3t16268H' => 'bol', 'BolC3t20879H' => 'bol', 'BolC4t25157H' => 'bol', 'BolC4t25177H' => 'bol', 'BolC4t25184H' => 'bol', 'BolC6t39331H' => 'bol', 'BolC6t39332H' => 'bol', 'BolC6t39333H' => 'bol', 'BolC6t39339H' => 'bol', 'BolC7t40807H' => 'bol', 'BolC7t43045H' => 'bol', 'BolC7t43046H' => 'bol', 'BolC7t43047H' => 'bol', 'BolC7t46484H' => 'bol', 'BolC9t54061H' => 'bol', 'BolC9t54311H' => 'bol', 'BraA02t07931Z' => 'bra', 'BraA03t12459Z' => 'bra', 'BraA03t15359Z' => 'bra', 'BraA04t16121Z' => 'bra', 'BraA07t27999Z' => 'bra', 'BraA07t29455Z' => 'bra', 'BraA07t31121Z' => 'bra', 'BraA07t31122Z' => 'bra', 'BraA07t31123Z' => 'bra', 'BraA07t31124Z' => 'bra', 'BraA08t33656Z' => 'bra', 'BraA09t36633Z' => 'bra', 'BraA09t36844Z' => 'bra', 'C03p40030' => 'bna', 'C03p85890' => 'bna', 'C04p36150' => 'bna', 'C04p36220' => 'bna', 'C04p36380' => 'bna', 'C06p40940' => 'bna', 'C06p40960' => 'bna', 'C06p40970' => 'bna', 'C06p40980' => 'bna', 'C07p04110' => 'bna', 'C07p25150' => 'bna', 'C07p25160' => 'bna', 'C07p25170' => 'bna', 'C07p25290' => 'bna', 'C07p60520' => 'bna', 'C09p11670' => 'bna', 'C09p14140' => 'bna', 'CAN.G322.110' => 'can', 'CAN.G914.2' => 'can', 'CANSAT01G1019' => 'cansat', 'CANSAT25G0801' => 'cansat', 'CARHR109220' => 'chi', 'CARHR242460' => 'chi', 'CARHR281050' => 'chi', 'CARHR281060' => 'chi', 'Carub.0002s0368' => 'cru', 'Carub.0003s3289' => 'cru', 'Carub.0005s0677' => 'cru', 'Carub.0005s0678' => 'cru', 'Carub.0005s0679' => 'cru', 'Carub.0005s0680' => 'cru', 'Carub.0005s0681' => 'cru', 'Carub.0005s0682' => 'cru', 'Carub.0007s0601' => 'cru', 'Carub.0007s0602' => 'cru', 'Carub.0007s0603' => 'cru', 'Carub.0007s0604' => 'cru', 'Carub.0008s2783' => 'cru', 'Carub.0008s2784' => 'cru', 'Carub.0077s0001' => 'cru', 'Carub.0077s0002' => 'cru', 'Ca_12488_v3' => 'car', 'Ca_12493_v3' => 'car', 'Ca_20848_v3' => 'car', 'Ca_24831_v3' => 'car', 'Ca_26382_v3' => 'car', 'Cc02_g17880' => 'ccan', 'Cc07_g05110' => 'ccan', 'CDE02G2454' => 'cde', 'CDE04G2283' => 'cde', 'CDE04G2931' => 'cde', 'Cfa004264' => 'cfa', 'Cfa004265' => 'cfa', 'Ciclev10025839m.g' => 'ccl', 'Ciclev10030403m.g' => 'ccl', 'CiPaw.01G032400' => 'cil', 'CiPaw.01G032500' => 'cil', 'CiPaw.01G032600' => 'cil', 'CiPaw.01G032700' => 'cil', 'CiPaw.01G032800' => 'cil', 'CiPaw.02G015000' => 'cil', 'CiPaw.05G061100' => 'cil', 'CiPaw.06G137800' => 'cil', 'ClCG02G001080' => 'cla', 'ClCG02G005280' => 'cla', 'ClCG09G017820' => 'cla', 'COL.COLO4_22143' => 'col', 'COL.COLO4_32460' => 'col', 'Cpa.g.sc158.19' => 'cpa', 'Cpa.g.sc62.111' => 'cpa', 'CsaV3_2G014410' => 'csa', 'CsaV3_2G017620' => 'csa', 'CsaV3_7G023240' => 'csa', 'CSS0014022' => 'camsi', 'CSS0030651' => 'camsi', 'CSS0045222' => 'camsi', 'DCAR_007517' => 'dca', 'DCAR_022099' => 'dca', 'DCAR_026266' => 'dca', 'Dinv23554' => 'din', 'Dinv26798' => 'din', 'Dinv31244' => 'din', 'Dinv39946' => 'din', 'Dinv42091' => 'din', 'Duzib132G1258' => 'dzi', 'Duzib147G0971' => 'dzi', 'Duzib187G0021' => 'dzi', 'Duzib248G0731' => 'dzi', 'Duzib264G0043' => 'dzi', 'ECA232G3025' => 'eca', 'ECA236G2604' => 'eca', 'ECA238G0922' => 'eca', 'ECA238G2579' => 'eca', 'EL10Ac6g14895' => 'bvu', 'EL10Ac6g14896' => 'bvu', 'EL10Ac9g21760' => 'bvu', 'Eucgr.G00464' => 'egr', 'Eucgr.G00466' => 'egr', 'Eucgr.G01899' => 'egr', 'Eucgr.G01902' => 'egr', 'Eucgr.G01903' => 'egr', 'Eucgr.H01229' => 'egr', 'Eucgr.H01230' => 'egr', 'Eucgr.H01231' => 'egr', 'Eucgr.H01233' => 'egr', 'Eucgr.H01234' => 'egr', 'Eucgr.H01914' => 'egr', 'Eucgr.H01915' => 'egr', 'Eucgr.H01916' => 'egr', 'Eucgr.H01918' => 'egr', 'Eucgr.H01920' => 'egr', 'Eucgr.H04971' => 'egr', 'Eucgr.I02475' => 'egr', 'Eucgr.L01953' => 'egr', 'Eucgr.L02021' => 'egr', 'Eucgr.L03059' => 'egr', 'Eucgr.L03147' => 'egr', 'Eucgr.L03393' => 'egr', 'FAN03G1277' => 'fan', 'FAN06G4360' => 'fan', 'FAN15G1788' => 'fan', 'FAN15G2740' => 'fan', 'FAN19G0364' => 'fan', 'FAN19G2196' => 'fan', 'FAN20G0697' => 'fan', 'FAN23G1338' => 'fan', 'FAN24G0963' => 'fan', 'FAN24G1400' => 'fan', 'FAN24G1401' => 'fan', 'FAN26G2905' => 'fan', 'FAN27G1516' => 'fan', 'FAN27G2863' => 'fan', 'FAN27G3112' => 'fan', 'FAN28G2585' => 'fan', 'FAN28G2884' => 'fan', 'FvH4_1g13660' => 'fve', 'FvH4_1g14080' => 'fve', 'FvH4_2g06181' => 'fve', 'FvH4_2g08070' => 'fve', 'FvH4_2g08100' => 'fve', 'FvH4_2g08180' => 'fve', 'FvH4_7g31862' => 'fve', 'Glyma.01G178400' => 'gma', 'Glyma.02G059100' => 'gma', 'Glyma.07G161300' => 'gma', 'Glyma.08G022700' => 'gma', 'Glyma.11G063800' => 'gma', 'Glyma.11G120500' => 'gma', 'Glyma.12G045600' => 'gma', 'Glyma.16G141800' => 'gma', 'Gohir.A02G163200' => 'ghi', 'Gohir.A02G163300' => 'ghi', 'Gohir.A02G163366' => 'ghi', 'Gohir.A02G163432' => 'ghi', 'Gohir.A02G163500' => 'ghi', 'Gohir.A02G163533' => 'ghi', 'Gohir.A03G180000' => 'ghi', 'Gohir.A12G066100' => 'ghi', 'Gohir.A13G048400' => 'ghi', 'Gohir.D02G202990' => 'ghi', 'Gohir.D03G016700' => 'ghi', 'Gohir.D03G016800' => 'ghi', 'Gohir.D03G016900' => 'ghi', 'Gohir.D03G017000' => 'ghi', 'Gohir.D03G017100' => 'ghi', 'Gohir.D03G017220' => 'ghi', 'Gohir.D12G066500' => 'ghi', 'Gohir.D13G046800' => 'ghi', 'Gorai.003G016900' => 'gra', 'Gorai.003G017000' => 'gra', 'Gorai.003G017100' => 'gra', 'Gorai.003G017200' => 'gra', 'Gorai.003G017300' => 'gra', 'Gorai.003G017400' => 'gra', 'Gorai.005G228900' => 'gra', 'Gorai.008G069800' => 'gra', 'Gorai.013G052500' => 'gra', 'GSVIVG01031916001' => 'vvi', 'HanXRQChr04g0128521' => 'han', 'HanXRQChr09g0272421' => 'han', 'HanXRQChr11g0331701' => 'han', 'HanXRQChr14g0452271' => 'han', 'HanXRQChr17g0557621' => 'han', 'Haze_02417' => 'cav', 'Haze_15136' => 'cav', 'Haze_15137' => 'cav', 'Hma1.2p1_0038F.1_g024280' => 'hma', 'Hma1.2p1_0066F.1_g036730' => 'hma', 'Hma1.2p1_0652F.1_g195940' => 'hma', 'Hma1.2p1_0652F.1_g195950' => 'hma', 'Hma1.2p1_0939F.1_g239410' => 'hma', 'HPP92_006925' => 'vpl', 'HPP92_009560' => 'vpl', 'HPP92_009561' => 'vpl', 'HPP92_024497' => 'vpl', 'Lalb_Chr01g0002721' => 'lal', 'Lalb_Chr03g0025811' => 'lal', 'Lalb_Chr05g0213001' => 'lal', 'Lalb_Chr09g0322661' => 'lal', 'Lalb_Chr17g0338191' => 'lal', 'Lj1g0023568' => 'lja', 'Lj2g0009408' => 'lja', 'Lj2g0019081' => 'lja', 'Lj3g0009377' => 'lja', 'Lj4g0017599' => 'lja', 'Lj5P200T42' => 'lonja', 'Lj7C11G2' => 'lonja', 'Lj7C11T1' => 'lonja', 'Lj7C11T3' => 'lonja', 'Lj7C11T4' => 'lonja', 'Lj9P366T23' => 'lonja', 'Lsat_1_v5_gn_2_86760' => 'lsa', 'Lsat_1_v5_gn_4_175700' => 'lsa', 'Lsat_1_v5_gn_7_89780' => 'lsa', 'Manes.12G098700' => 'mes', 'Manes.13G136100' => 'mes', 'Manes.15G148300' => 'mes', 'Manes.17G099100' => 'mes', 'Mapoly0036s0046' => 'mpo', 'MBI16_g13143_MAGBIO' => 'mbi', 'MBI16_g33267_MAGBIO' => 'mbi', 'MBI16_g33269_MAGBIO' => 'mbi', 'MBI16_g34926_MAGBIO' => 'mbi', 'MBI16_g34929_MAGBIO' => 'mbi', 'MBI16_g41853_MAGBIO' => 'mbi', 'MBI16_g41854_MAGBIO' => 'mbi', 'MBI16_g44439_MAGBIO' => 'mbi', 'MBI16_g44440_MAGBIO' => 'mbi', 'MD02G1154800' => 'mdo', 'MD05G1070600' => 'mdo', 'MD10G1081600' => 'mdo', 'MD11G1180100' => 'mdo', 'MD15G1269200' => 'mdo', 'Medtr1g034480' => 'mtr', 'Medtr3g011140' => 'mtr', 'Medtr4g069160' => 'mtr', 'Medtr5g019430' => 'mtr', 'Medtr8g078100' => 'mtr', 'MELO3C012570.2' => 'cme', 'MELO3C020955.2' => 'cme', 'MELO3C021948.2' => 'cme', 'Migut.B00265' => 'egut', 'Migut.H00526' => 'egut', 'Migut.K00856' => 'egut', 'Migut.O00625' => 'egut', 'Migut.O00626' => 'egut', 'MSTRG.16791' => 'ama', 'MSTRG.2937' => 'ama', 'MSTRG.3391' => 'ama', 'MSTRG.5390' => 'ama', 'Nitab4.5_0000107g0040' => 'nta', 'Nitab4.5_0000199g0020' => 'nta', 'Nitab4.5_0002622g0020' => 'nta', 'Nitab4.5_0004280g0090' => 'nta', 'Nitab4.5_0012349g0020' => 'nta', 'Nn1g04448' => 'nnu', 'Nn1g05097' => 'nnu', 'Nn2g14667' => 'nnu', 'Nn2g15721' => 'nnu', 'Nn5g27121' => 'nnu', 'Nn5g29497' => 'nnu', 'Oeu003715.1' => 'oeu', 'Oeu003716.1' => 'oeu', 'Oeu011852.1' => 'oeu', 'Oeu021893.2' => 'oeu', 'Oeu021894.1' => 'oeu', 'Oeu021899.1' => 'oeu', 'Oeu027314.1' => 'oeu', 'Oeu033433.1' => 'oeu', 'Oeu033439.1' => 'oeu', 'Oeu038871.1' => 'oeu', 'Oeu049324.1' => 'oeu', 'Oeu063121.1' => 'oeu', 'Os03g0199100' => 'osa', 'Os10g0359200' => 'osa', 'Peaxi162Scf00016g00102' => 'pax', 'Peaxi162Scf00078g00011' => 'pax', 'Peaxi162Scf00078g00013' => 'pax', 'Peaxi162Scf00078g00021' => 'pax', 'Peaxi162Scf00078g10022' => 'pax', 'Peaxi162Scf00684g00568' => 'pax', 'Peaxi162Scf01900g00001' => 'pax', 'PGR042G0862' => 'pgr', 'PGR042G1664' => 'pgr', 'PGR102G0101' => 'pgr', 'PGR102G2588' => 'pgr', 'PGR119G0674' => 'pgr', 'PGR142G0474' => 'pgr', 'PGR142G1810' => 'pgr', 'PGSC0003DMG400025185' => 'stu', 'PGSC0003DMG400037697' => 'stu', 'Phvul.002G026300' => 'pvu', 'Phvul.003G010400' => 'pvu', 'Phvul.011G047500' => 'pvu', 'Potri.004G150800' => 'ptr', 'Potri.005G127200' => 'ptr', 'Potri.005G127300' => 'ptr', 'Potri.005G127401' => 'ptr', 'Potri.007G031200' => 'ptr', 'Potri.009G112430' => 'ptr', 'Potri.T125304' => 'ptr', 'Pp3c9_13670' => 'ppa', 'Prupe.7G148500' => 'ppe', 'Prupe.8G103100' => 'ppe', 'Prupe.8G103700' => 'ppe', 'Psat2g162280' => 'psa', 'Psat4g091120' => 'psa', 'Psat5g203480' => 'psa', 'Psat6g097400' => 'psa', 'Psat7g184960' => 'psa', 'PSO017G3430' => 'pso', 'PSO170G0924' => 'pso', 'PSO170G6266' => 'pso', 'PSO700G0028' => 'pso', 'QL06p044956' => 'qlo', 'QL11p042349' => 'qlo', 'RcHm_v2.0_Chr0c38g0503041' => 'rch', 'RcHm_v2.0_Chr0c38g0503061' => 'rch', 'RcHm_v2.0_Chr0c38g0503091' => 'rch', 'RcHm_v2.0_Chr2g0102731' => 'rch', 'RcHm_v2.0_Chr2g0102741' => 'rch', 'RcHm_v2.0_Chr4g0395591' => 'rch', 'RcHm_v2.0_Chr4g0419891' => 'rch', 'RcHm_v2.0_Chr4g0420001' => 'rch', 'RcHm_v2.0_Chr6g0262571' => 'rch', 'RcHm_v2.0_Chr6g0262781' => 'rch', 'RcHm_v2.0_Chr6g0262911' => 'rch', 'RcHm_v2.0_Chr6g0262961' => 'rch', 'RcHm_v2.0_Chr6g0265941' => 'rch', 'Rhsim05G0076700' => 'rsi', 'Rhsim08G0111500' => 'rsi', 'Rhsim11G0173400' => 'rsi', 'Sabra04G0100300' => 'sbr', 'Sabra07G0027100' => 'sbr', 'Sabra09G0085800' => 'sbr', 'SalBow1G0930' => 'sbo', 'SalBow1G3979' => 'sbo', 'SalBow1G4203' => 'sbo', 'SalBow1G5021' => 'sbo', 'SalBow1G7782' => 'sbo', 'SalBow2G3417' => 'sbo', 'SalBow3G1146' => 'sbo', 'SalBow4G2581' => 'sbo', 'SalBow5G4977' => 'sbo', 'SalBow5G5572' => 'sbo', 'SalBow5G5721' => 'sbo', 'SalBow6G0914' => 'sbo', 'SalBow6G1209' => 'sbo', 'SalBow8G0128' => 'sbo', 'SalBow8G1687' => 'sbo', 'Sc16g0001080' => 'sci', 'Sc16g0001180' => 'sci', 'Sc16g0001390' => 'sci', 'Sc16g0001470' => 'sci', 'Sc18g0004680' => 'sci', 'Sc18g0004690' => 'sci', 'Sed0014401' => 'sed', 'Sed0022138' => 'sed', 'Sed0023195' => 'sed', 'SEGI_10473' => 'sgi', 'SEGI_20859' => 'sgi', 'SEGI_22549' => 'sgi', 'SEGI_23198' => 'sgi', 'SEGI_37129' => 'sgi', 'SEGI_40369' => 'sgi', 'SGA_v2.0_scaffold10G05131' => 'sas', 'SGA_v2.0_scaffold13G06564' => 'sas', 'SGA_v2.0_scaffold204G41646' => 'sas', 'SHI05436' => 'shi', 'SMO275G0004' => 'smo', 'SMO275G0037' => 'smo', 'SMO367G0681' => 'smo', 'SMO367G1038' => 'smo', 'SMO367G1236' => 'smo', 'Solyc01g016580.1' => 'sly', 'Solyc01g016600.2' => 'sly', 'Solyc01g109380.3' => 'sly', 'Solyc11g039740.3' => 'sly', 'Sopen01g051570' => 'spe', 'Sopen11g015460' => 'spe', 'Sp2g30030' => 'spa', 'Sp2g30040' => 'spa', 'Sp3g32120' => 'spa', 'Sp5g06200' => 'spa', 'Sp7g32120' => 'spa', 'TAR376G0890' => 'tar', 'TAR381G1191' => 'tar', 'TAR628G0219' => 'tar', 'TAR628G1290' => 'tar', 'TAR628G1472' => 'tar', 'THA.LOC104800220' => 'tha', 'THA.LOC104802200' => 'tha', 'THA.LOC104807331' => 'tha', 'THA.LOC104808428' => 'tha', 'THA.LOC104809771' => 'tha', 'THA.LOC104809885' => 'tha', 'THA.LOC104809898' => 'tha', 'THA.LOC104810142' => 'tha', 'THA.LOC104810155' => 'tha', 'THA.LOC104810156' => 'tha', 'THA.LOC104821282' => 'tha', 'THA.LOC104821283' => 'tha', 'THA.LOC104826854' => 'tha', 'THA.LOC109116534' => 'tha', 'Thecc.01G041800' => 'tca', 'Thecc.02G122100' => 'tca', 'Thhalv10001140m.g' => 'esa', 'Thhalv10004318m.g' => 'esa', 'Thhalv10005400m.g' => 'esa', 'Thhalv10022714m.g' => 'esa', 'Thhalv10025525m.g' => 'esa', 'Thhalv10027573m.g' => 'esa', 'TPR.G18598' => 'tpr', 'TPR.G20277' => 'tpr', 'TPR.G23217' => 'tpr', 'TPR.G28054' => 'tpr', 'TWI09G0356' => 'twi', 'TWI31G1269' => 'twi', 'TWI53G1697' => 'twi', 'TWI73G0528' => 'twi', 'TWI75G0560' => 'twi', 'TWI79G1335' => 'twi', 'unitig_22.g5413' => 'ugi', 'unitig_52.g17622' => 'ugi', 'unitig_62.g23400' => 'ugi', 'unitig_747.g21217' => 'ugi', 'vmacro02137' => 'vma', 'vmacro02139' => 'vma', 'vmacro02140' => 'vma', 'vmacro02141' => 'vma', 'vmacro02142' => 'vma', 'vmacro02187' => 'vma', 'vmacro23071' => 'vma', 'vmacro23072' => 'vma', 'vmacro23075' => 'vma', 'VMungo1127G0164' => 'vmu', 'VMungo1215G1120' => 'vmu', 'VMungo1215G2091' => 'vmu', 'Zm00001eb007920' => 'zma', 'Zm00001eb400890' => 'zma', 'Zm00001eb400920' => 'zma' ) $gf_id = 'HOM05D001084' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001084' ) $data_identifier = 'HOM05D001084' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 29, 'aar' => (int) 4, 'aag' => (int) 3, 'ach' => (int) 9, 'amhyb' => (int) 2, 'aly' => (int) 12, 'aox' => (int) 3, 'arhy' => (int) 2, 'ath' => (int) 12, 'atr' => (int) 1, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 27, 'bol' => (int) 16, 'bra' => (int) 13, 'can' => (int) 2, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 16, 'car' => (int) 5, 'ccan' => (int) 2, 'cde' => (int) 3, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 8, 'cla' => (int) 3, 'col' => (int) 2, 'cpa' => (int) 2, 'csa' => (int) 3, 'camsi' => (int) 3, 'dca' => (int) 3, 'din' => (int) 5, 'dzi' => (int) 5, 'eca' => (int) 4, 'bvu' => (int) 3, 'egr' => (int) 22, 'fan' => (int) 17, 'fve' => (int) 7, 'gma' => (int) 8, 'ghi' => (int) 18, 'gra' => (int) 9, 'vvi' => (int) 1, 'han' => (int) 5, 'cav' => (int) 3, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 5, 'lja' => (int) 5, 'lonja' => (int) 6, 'lsa' => (int) 3, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 9, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 3, 'egut' => (int) 5, 'ama' => (int) 4, 'nta' => (int) 5, 'nnu' => (int) 6, 'oeu' => (int) 12, 'osa' => (int) 2, 'pax' => (int) 7, 'pgr' => (int) 7, 'stu' => (int) 2, 'pvu' => (int) 3, 'ptr' => (int) 7, 'ppa' => (int) 1, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 2, 'rch' => (int) 13, 'rsi' => (int) 3, 'sbr' => (int) 3, 'sbo' => (int) 15, 'sci' => (int) 6, 'sed' => (int) 3, 'sgi' => (int) 6, 'sas' => (int) 3, 'shi' => (int) 1, 'smo' => (int) 5, 'sly' => (int) 4, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 5, 'tha' => (int) 14, 'tca' => (int) 2, 'esa' => (int) 6, 'tpr' => (int) 4, 'twi' => (int) 6, 'ugi' => (int) 4, 'vma' => (int) 9, 'vmu' => (int) 3, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb400920' $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